Contacts of the strand formed by residues 95 - 98 (chain M) in PDB entry 1W72
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with HIS 95 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47I TRP* 3.8 9.6 - + - -
59I TYR 4.5 2.0 - - - -
60I ALA* 3.5 20.5 - - - +
61I ASP* 3.0 55.5 + - - +
64I LYS* 4.9 2.5 - - - -
91M TRP* 3.4 7.3 - + - -
92M ASP* 3.0 30.2 + - + -
95M ASP* 1.3 115.0 + - - +
96M TRP* 1.3 68.2 - - - -
97M VAL* 3.8 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 96 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35I HIS* 3.6 4.4 - + - -
47I TRP* 3.5 65.1 + + + +
100I MET* 2.8 103.2 + + - -
34M HIS* 4.4 7.2 - + - -
89M GLN* 3.2 37.5 - - + +
90M VAL 3.6 4.9 - - - -
91M TRP* 3.5 46.6 - + + -
95M HIS* 1.3 81.6 - - - -
97M VAL* 1.3 59.0 + - - +
98M PHE* 4.4 1.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 97 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2M TYR* 3.4 42.4 - - + +
3M VAL* 4.7 0.2 - - - -
4M LEU* 3.7 22.2 - - + +
89M GLN* 3.1 5.7 - - - +
90M VAL* 2.8 48.7 + - + +
92M ASP* 4.4 7.0 - - + -
95M HIS* 4.0 20.4 - - + +
96M TRP* 1.3 78.1 - - - +
98M PHE* 1.3 70.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 98 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37I VAL* 3.9 15.9 - - + -
45I LEU* 3.4 60.8 - - + +
46I GLU* 4.2 0.4 - - - -
47I TRP* 3.7 31.6 - - + -
103I TRP* 4.1 7.4 - + - -
4M LEU* 4.2 6.8 + - - +
36M TYR* 4.1 10.5 - + - -
87M TYR* 4.3 7.0 - - + -
88M CYS 3.3 8.7 - - - -
89M GLN* 3.2 42.8 - - + -
96M TRP* 5.2 0.7 - - + -
97M VAL* 1.3 83.3 - - - +
99M GLY* 1.3 71.3 + - - +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il